I can not remove my enchanted boots manually (Windows 10). My diamond boots are enchanted with depth strider 3, protection 4, soul speed 3, feather falling 4, thorns 3, in breaking 3 and mending. 
the only way I have been able to remove them is by left clicking while holding another pair of boots to equip those. I have had no issues removing boots I have put on using left click. My assumption is that souls speed is the culprit.